Thank you for sending a sample dojo with the issue isolated. I noticed the dojo follows the example on Gantt Task Templates, with one styling difference:
background: rgba(0, 0, 0, .3);
In the dojo provided the height is set to 100% thus the progress element covers the close icon when the task is 100% completed. You could either set a height for .progress class so that it is lower than the close icon or adjust the z-index of the close icon:
Here is a dojo that demonstrates the above approach.
Let me know if you have further questions.